Dear Bruce,
thank you so much for your reply; it seems to work now.
However, a weird thing, I also mentioned in my previous post, still happens: when using ic3 there are duplicate labels in the newly created annotations.
at least the following labelnames are given to two spatially separated labels. ic3.tri_vertex_25 (in fsaverage lh: cluster 1 around vertex 41132, cluster 2 around vertex 157199) ic3.tri_vertex_42 (in fsaverage lh: cluster 1 around vertex 137845, cluster 2 around vertex 155417)
Is there a way to avoid this?
Thanks for your help, Franz
Am 26.01.2012 um 14:47 schrieb Bruce Fischl:
Hi Franz
looks like this was a bug in mris_make_face_parcellation, which I just fixed. It was always using the sphere regardless of what you specified. Krish: can you get Franz a new mac version of it to try out?
sorry Bruce
On Thu, 26 Jan 2012, Franz Liem wrote:
Dear Freesurfers,
I have some questions regarding mris_make_face_parcellation (and possibly found one error in the .tri file). (I am working with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0).
I would like to make a high res parcellation of several subjects and used ic3.tri. Parcels should correspond across subjects. I computed mris_make_face_parcellation ../surf/lh.sphere $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot
- It seems not to make a difference whether I choose .sphere or .sphere.reg as input, the resulting parcellations are identical (i checked by comparing vertex label values in matlab; .inflated deviates a bit, but not substantially).
According to Bruce (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18509.html): "You want to use either ?h.sphere if you want it to be uniform in subject space or ?h.sphere.reg if you want the parcels to correspond across subjects"
Could anybody tell me how the parcellation is performed exactly? I thought it was performed on the input surf (the input surf is parcellated into (e.g.) 642 equally sized parcels), which should lead to different results at .sphere and .sphere.reg, shouldn't it?
Alternatively, would it be better to mris_make_face_parcellation the fsaverage and mri_surf2surf the high res parcellation onto each subject to get cross-subject correspondency (I tried this. It didn't look that great with this command: mri_surf2surf --srcsubject fsaverage --sval-annot ic3.annot --trgsubject subject1 --tval ic3s03.annot --hemi lh )?
To recap, what is the best strategy to arrive with cross-subject-corresponing parcellations? Performing mris_make_face_parcellation with ?h.sphere.reg for each subject individually?
- There seems to be duplicate structNames/annotationValues when applying mris_make_face_parcellation with ic3.tri
In fsaverage at least the following labelnames are given to two spatially separated labels. ic3.tri_vertex_25 (cluster 1 around vertex 41132, cluster 2 around vertex 157199) ic3.tri_vertex_42 (cluster 1 around vertex 137845, cluster 2 around vertex 155417) How come?
Thanks for you help, Franz
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